Many investigators designing antisense oligonucleotides or ribozymes to inhibit specific RNA's generally avoid targeting regions with strong secondary structure to facilitate hybridization. E. Wickstrom, W. S. Simonet, K. Medlock, I. Ruiz-Robles, Biophys. J. 49, 15 (1986). However, structured RNA's generally contain single stranded portions which are available for base pairing; there may be thermodynamic, kinetic or functional advantages to targeting these regions. For example, natural antisense recognition systems in E. coli involve bimolecular interactions between two highly structured hairpin loops which have fast hybridization rates. Y. Eguchi, T. Itoh, J. Tomizawa, Annu. Rev. Biochem. 60, 631 (1991).
Specific regulatory proteins often recognize structured RNA regions such as the HIV TAR and RRE elements. C. Dingwall, I. Ernberg, M. J. Gait, et al, Proc. Natl. Acad. Sci. USA 86, 6925 (1989); C. Dingwall, I. Ernberg, M. J. Gait, et al, EMBO J. 9, 4145 (1990); S. Roy, U. Delling, C.-H. Chen, C. A. Rosen, N. Sonenberg, Genes Dev. 4, 1365 (1990); C. A. Rosen, G. N. Pavlakis, AIDS 4,499 (1990); K. M. Weeks, C. Ampe, S. C. Schultz, T. A. Steitz, D. M. Crothers, Science 249, 1281 (1990), the iron responsive element in mammalian cells, J. L. Casey, M. W. Hentze, D. M. Koeller, et al, Science 240, 924 (1988), and the R17 phage coat protein, G. W. Witherell, H.-N. Wu, O. C. Uhlenbeck, Biochemistry 29, 11051 (1990).
RNA viruses contain capsid proteins which specifically package only the viral genome by binding to structured RNA regions, M. Junker-Niepmann, R. Bartenschlager, H. Schaller, EMBO J. 9, 3389 (1990). Enhanced biological specificity can be obtained by targeting these regions. The cell will contain many non-targetRNA sequences to which the antisense compounds are either closely or precisely complementary. Although ribozymes bind and cleave their target RNA, other antisense molecules do not cleave their target and may not produce significant biological effects unless they compete effectively with a biomolecule for the target site. There are currently no reliable methods for determining accessible target sites.
In view of the potential advantages of binding to structured RNA's, compositions and methods for binding to structured regions are desired.